[gmx-users] Question about gcc version
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 29 16:51:17 CEST 2008
Justin A. Lemkul wrote:
>>> Thanks David. I ran the test set, and got the following:
>>> $ ./gmxtest.pl all
>>> No topol.tpr file in morse. grompp failed
>>> FAILED. Check files in morse
>>> 1 out of 16 simple tests FAILED
>>> FAILED. Check files in dec+water
>>> 1 out of 14 complex tests FAILED
>>> All 63 kernel tests PASSED
>>> Error not all 45 pdb2gmx tests have been done successfully
>>> Only 38 energies in the log file
>>> For the "No topol.tpr file in morse" error, the grompp.out file shows:
>>> Fatal error:
>>> number of coordinates in coordinate file (conf.gro, 1490)
>>> does not match topology (topol.top, 0)
>>> ...although I'm not sure why.
>> Look further up in the grompp.out file
> Alright, I tracked this one down to the fact that the "include" line was
> pointing to a non-existent directory (/home/gmx/top). I changed that in the
> grompp.mdp and all is well.
>>> The dec+water failure has been discussed before, although the discrepancy
>>> slightly different than that listed on the wiki:
>>> There are 5 terms to compare in the energy files
>>> LJ (SR) step 34: -0.21167, step 34: -0.171631
>>> The pdb2gmx.log file shows that there is some discrepancy in the .mdp
>>> WARNING 1 [file ../../../../em.mdp, line unknown]:
>>> Unknown left-hand 'bd-temp' in parameter file
>>> checking input for internal consistency...
>>> processing coordinates...
>>> Program grompp, VERSION 3.3.3
>>> Source code file: futil.c, line: 345
>>> File input/output error:
>>> I'm guessing this is just a reflection of changes that have been made
>>> versions 3.3.2 and 3.3.3? But I don't know what to make of the "38
>> energies in
>>> log file." Is there some more relevant output I can post to help clarify
>> Again, here you may need to look more closely in the output file. If
>> b4em.gro does not exist something went wrong before.
> This error seemed a bit more worrisome. It turns out that the initial pdb2gmx
> conversion to conf.gro failed, giving a similar error to one that I reported in
> a bugzilla not too long ago (http://bugzilla.gromacs.org/show_bug.cgi?id=171).
> This time around, pdb2gmx complained:
> Fatal error:
> Atom H not found in residue 2 while adding improper
> It turned out that (in the bug report) the Gromacs installation was from a
> broken Ubuntu package on that particular machine. Looks like using gcc 4.0.1
> might result in a similarly broken package in this case. I have installed
> gcc-3.3, used it to re-compile Gromacs 3.3.3, and all the tests pass except for
> the dec+water, which seems OK to me.
If it works it works, but anyone using a Mac has gcc-4.0.x (including
me). Mixing of packages could be an explanation.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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